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Protein

Acyl-CoA thioesterase YbgC

Gene

ybgC

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Thioesterase that may be involved in phospholipid metabolism. Displays acyl-CoA thioesterase activity with lauroyl-CoA (C12:0), myristoyl-CoA (C14:0), palmitoyl-CoA (C16:0), stearoyl-CoA (C18:0) and benzoyl-CoA, catalyzing the hydrolysis of the thioester bond. Has low activity with butyryl-CoA and octanoyl-CoA.1 Publication

Kineticsi

kcat is 0.028 sec(-1) with benzoyl-CoA, 0.034 sec(-1) with stearoyl-CoA, 0.045 sec(-1) with palmitoyl-CoA, 0.024 sec(-1) with myristoyl-CoA, 0.015 sec(-1) with lauroyl-CoA and 0.0013 sec(-1) with octanoyl-CoA.

  1. KM=200 µM for benzoyl-CoA
  2. KM=210 µM for stearoyl-CoA
  3. KM=570 µM for palmitoyl-CoA
  4. KM=240 µM for myristoyl-CoA
  5. KM=160 µM for lauroyl-CoA
  6. KM=40 µM for octanoyl-CoA
  7. KM=27 µM for butyryl-CoA

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei11 – 111PROSITE-ProRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Lipid metabolism

    Enzyme and pathway databases

    BioCyciHPY:HP0496-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Acyl-CoA thioesterase YbgC (EC:3.1.2.-)
    Gene namesi
    Name:ybgC
    Ordered Locus Names:HP_0496
    OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
    Taxonomic identifieri85962 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
    Proteomesi
    • UP000000429 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 133133Acyl-CoA thioesterase YbgCPRO_0000087767Add
    BLAST

    Proteomic databases

    PaxDbiP94842.
    PRIDEiP94842.

    Interactioni

    Subunit structurei

    Homotetramer. May interact with CagA.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    cagAP559802EBI-528090,EBI-528104

    Protein-protein interaction databases

    DIPiDIP-3437N.
    IntActiP94842. 1 interaction.
    MINTiMINT-167425.
    STRINGi85962.HP0496.

    Structurei

    Secondary structure

    133
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 44Combined sources
    Helixi7 – 93Combined sources
    Beta strandi14 – 163Combined sources
    Helixi20 – 3415Combined sources
    Turni35 – 373Combined sources
    Beta strandi40 – 423Combined sources
    Beta strandi45 – 5612Combined sources
    Beta strandi65 – 7511Combined sources
    Beta strandi77 – 9014Combined sources
    Beta strandi100 – 11213Combined sources
    Turni114 – 1163Combined sources
    Helixi124 – 1318Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PZHX-ray1.70A/B/C/D1-133[»]
    ProteinModelPortaliP94842.
    SMRiP94842. Positions 1-132.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP94842.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107YD3. Bacteria.
    COG0824. LUCA.
    KOiK07107.
    OMAiRIVDCNG.
    OrthoDBiEOG6JQH7N.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    InterProiIPR008272. HB-CoA_thioesterase_AS.
    IPR029069. HotDog_dom.
    IPR006683. Thioestr_dom.
    IPR006684. YbgC/YbaW.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003230. YbgC. 1 hit.
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00051. TIGR00051. 1 hit.
    PROSITEiPS01328. 4HBCOA_THIOESTERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P94842-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRCRVYYEDT DSEGVVYHAN YLKYCERARS EFFFKQNVLP ENEEGVFVIR
    60 70 80 90 100
    SIKADFFTPA SLGQVLEIRT QIKELRKVFV VLFQEIYCIQ NASLEPMKPF
    110 120 130
    KVFASEIKFG FVNRSTYSPI AIPKLFKELL NAI
    Length:133
    Mass (Da):15,596
    Last modified:July 15, 1999 - v2
    Checksum:i18C969BB96B802F9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti133 – 1331I → V in AAB39716 (Ref. 1) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U75328 Genomic DNA. Translation: AAB39716.1.
    AE000511 Genomic DNA. Translation: AAD07561.1.
    PIRiH64581.
    RefSeqiNP_207293.1. NC_000915.1.
    WP_001203797.1. NC_018939.1.

    Genome annotation databases

    EnsemblBacteriaiAAD07561; AAD07561; HP_0496.
    GeneIDi900055.
    KEGGiheo:C694_02550.
    hpy:HP0496.
    PATRICi20592267. VBIHelPyl33062_0522.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U75328 Genomic DNA. Translation: AAB39716.1.
    AE000511 Genomic DNA. Translation: AAD07561.1.
    PIRiH64581.
    RefSeqiNP_207293.1. NC_000915.1.
    WP_001203797.1. NC_018939.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PZHX-ray1.70A/B/C/D1-133[»]
    ProteinModelPortaliP94842.
    SMRiP94842. Positions 1-132.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-3437N.
    IntActiP94842. 1 interaction.
    MINTiMINT-167425.
    STRINGi85962.HP0496.

    Proteomic databases

    PaxDbiP94842.
    PRIDEiP94842.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD07561; AAD07561; HP_0496.
    GeneIDi900055.
    KEGGiheo:C694_02550.
    hpy:HP0496.
    PATRICi20592267. VBIHelPyl33062_0522.

    Phylogenomic databases

    eggNOGiENOG4107YD3. Bacteria.
    COG0824. LUCA.
    KOiK07107.
    OMAiRIVDCNG.
    OrthoDBiEOG6JQH7N.

    Enzyme and pathway databases

    BioCyciHPY:HP0496-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP94842.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    InterProiIPR008272. HB-CoA_thioesterase_AS.
    IPR029069. HotDog_dom.
    IPR006683. Thioestr_dom.
    IPR006684. YbgC/YbaW.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    PIRSFiPIRSF003230. YbgC. 1 hit.
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00051. TIGR00051. 1 hit.
    PROSITEiPS01328. 4HBCOA_THIOESTERASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Sequence of the dihydrodipicolinate reductase gene (dapB) from Helicobacter pylori and complementation in Escherichia coli."
      Clairoux N., Boissinot M.
      Submitted (OCT-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: DSM 4867 / CCUG 17874 / NCTC 11638.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700392 / 26695.
    3. "Biochemical characterization of protein complexes from the Helicobacter pylori protein interaction map: strategies for complex formation and evidence for novel interactions within type IV secretion systems."
      Terradot L., Durnell N., Li M., Li M., Ory J., Labigne A., Legrain P., Colland F., Waksman G.
      Mol. Cell. Proteomics 3:809-819(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CAGA.
    4. "Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori."
      Angelini A., Cendron L., Goncalves S., Zanotti G., Terradot L.
      Proteins 72:1212-1221(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS), FUNCTION, SUBUNIT.

    Entry informationi

    Entry nameiYBGC_HELPY
    AccessioniPrimary (citable) accession number: P94842
    Secondary accession number(s): O25238
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: July 15, 1999
    Last modified: March 16, 2016
    This is version 105 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Helicobacter pylori
      Helicobacter pylori (strain 26695): entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.